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732DefectSkylineExporting user-defined reports from command lineBrendan MacLean3resolved 
731DefectSkylineVarying small molecule implementations of .MSP format aren't handled well by SkylineBrian Pratt3open 
730DefectSkylinePeak MS1 integration with FAIMSmatt.chambers42@gmail.com2open 
729DefectSkylineConfusing progress indicator behavior on SRM import when targeted transitions are less intense than other unmatched transitions - it just shows greyBrian Pratt3open 
728DefectSkylineAutoQC: retry upload to Panorama if upload fails due to network errorVagisha3open 
727DefectSkylinePanorama upload issuesVagisha3open20.2
726DefectBiblioSpecSkyline nonredundant blib format to MS2 conversionmatt.chambers42@gmail.com3resolved 
725DefectSkylineNeed to improve inference of ionization type when reading small molecule .MSP filesBrian Pratt3resolved 
724DefectSkylineImport multiple files as a single run for iRT calibrationKaipo3open20.2
723DefectSkylinePrecursors per sample injection think's it is transitions per sample injectionBrendan MacLean3open 
722DefectSkylineHow can I put z+1 ions in the fragments list for ETD?Brendan MacLean3open 
721DefectSkylineSkyline cannot properly analyze Agilent QQQ with waste diverter in the beginning of the runBrendan MacLean3open 
720DefectSkylineUpload to Panorama fails when There are custom annotations for the TransitionsBrendan MacLean3resolved 
719DefectSkylineCalibration curve of Sodiated Adduct not appearingBrian Pratt3resolved 
718TodoSkylineAllow overlay of QC traces on chromatogramsBrendan MacLean3open 
717DefectSkylineImprove handling of unknown adducts in small molecule transition reader (exception on seeing adduct "[+]" not caught gracefully)Brian Pratt3open 
716DefectSkylineWhen light and heavy precursors have different sets of transitions, all quantifiable transitions should be summed when calculating Light:Heavy ratiosNick Shulman3open20.2
715DefectSkylineProsit not availableBrendan MacLean3open 
714DefectSkylineQuestion about Data upload to panoramaGuest3closed 
713DefectSkylineUnable to view or explore spectral libraries in Skyline DailyNick Shulman3open 
712DefectSkylineAcetyl 2H(3) K modification disappears on heavy en medium peptides, when library is created from Maxquantmatt.chambers42@gmail.com2resolved 
711DefectSkylineTroubles with skyline document file upload to LabKey ServerVagisha3open 
710DefectSkylineSkyline Unistall problemsGuest3closed 
709DefectSkylinePotentially possible to do a better job at routing external tool support requests to tool-specific support boardsBrendan MacLean4open 
708DefectSkylineRenaming a molecule in Targets tree causes Skyline to miscalculate mass of transition with heavy label adductBrian Pratt3resolved19.2
707DefectSkylineDefault report names stuck in installation languageNick Shulman3open 
706DefectSkylinePeptide data not imported for a few peptidesBrendan MacLean3open 
705DefectSkylineToo much audit logging for Refine > Accept PeptidesNick Shulman3open 
704DefectSkylineSkyline silently fails reading FASTA files with sequences in lowercaseBrian Pratt3open 
703DefectSkylineNightly tutorial tests should not always re-download data sets - makes us too vulnerable to temporary outagesBrian Pratt3open 
702DefectSkylineIllegal character is phosphopeptide sequenceBrendan MacLean3resolved 
701DefectSkylineMalfunctioning of the reintegration toolBrendan MacLean3resolved 
700DefectSkylineMalfunctioning of the reintegration toolGuest3closed 
699DefectSkylineMalfunctioning of the reintegration toolGuest3closed 
698TodoSkylineAdd Mass Errors to Spectrum Match graphritach3open 
697DefectSkylineimport wizard should not ask about ion mobility handling if the files to be imported don't contain any IM infoBrian Pratt3open 
696DefectSkylinelibrary filename extensions are case sensitive (e.g. Skyline recognizes "foo.msp" but not "foo.MSP")Brian Pratt3resolved19.2
695DefectSkylineFailed importing results DIAGuest3closed 
694DefectSkylineAudit Log records a failed operation and does not roll it backTobias Rohde3open 
693TodoSkylineImprove "Apply Peak to All" peak matchingKaipo3open 
692TodoSkylineChange some default settingsBrendan MacLean3open19.2
691DefectSkylineLimiting Transition Settings - Instrument - Max m/z has unintended consequences on spectral library transition pickingKaipo2open19.2
690DefectSkylineBefore starting a new Import > Results we need to check that Decoys are representative of the TargetsKaipo2open19.2
689DefectSkylineFile > Export > Spectral Library losing information from small molecule documentsBrian Pratt2open19.2
688TodoSkylineAdd Product Loss Formula column to Edit > Insert > Transitions for small moleculesBrian Pratt2open19.2
687TodoSkylineImplement support for charged losses where Skyline currently has only neutral lossesBrendan MacLean2resolved19.2
686TodoSkylineImplement a better system for assigning a version which is not web installedmatt.chambers42@gmail.com2open19.2
685DefectSkylineShow progress in LongWaitDlg for Skyline document import on PanoramaVagisha3resolved19.2
684DefectSkylineDo not use getContainers to determine if a URL is for a LabKey ServerVagisha3open19.2
683TodoSkylineAdd support for opening .skyp files in SkylineVagisha3resolved19.2
682DefectSkylineImport peptide search from Start page differs from File > Import > Peptide SearchBrendan MacLean2resolved19.1
681TodoSkylineExport method sorted by m/zKaipo3resolved 
680TodoSkylineAdd access to some of the explicit values added for small molecules to peptide transition list importBrendan MacLean3open 
679TodoSkylineMake drift time predictor training available for use from command-lineBrian Pratt3open 
678DefectSkylineUnhandled error when importing peak boundaries for document with no result filesNick Shulman4open 
677TodoSkylineAdd PEP (localFDR) as another score beside q values for mProphet picked peaksKaipo3open 
675TodoSkylineView > Proteins and View > Peptides menu items added and remove View > TargetsBrendan MacLean2resolved19.2
674TodoSkylineWork out a way for an interactive tool to know Skyline is closing or has closedBrendan MacLean3open19.2
673DefectSkylineOrder By > Annotation in summary plots got brokenBrendan MacLean2resolved19.1
672DefectSkylineQuerying UniProt for SGD Yeast FASTA information having problemsBrendan MacLean1resolved19.2
671TodoSkylineImprove small molecule peak boundaries importBrian Pratt3open19.2
670DefectSkylineSkylineTester's tutorial demo mode should roll forever, and slow down a bitBrian Pratt3open 
669TodoSkylineConsider adding explicit window size for CCS and/or IM for transition list importBrian Pratt3open19.2
668DefectSkylineUI mode selection capability should be available in the menu systemBrian Pratt3open19.2
667DefectSkylineInclude fragment ion annotation when "Copy Data" from Library Match tabBrendan MacLean3open 
666DefectSkylineThe "Add small molecule test nodes" checkbox on SkylineTester is obsolete and confusing, should be removedBrian Pratt3resolved 
665DefectSkylineReplicate Label Fonts on Graph Axis too smallBrendan MacLean3resolved 
664TodoSkylineAdd "Only max precursor peak" checkbox below "Max peptide peak rank" field in Refine > Advanced - Results tabpvvemul3open19.2
662TodoSkylineAdd View > Peptides > By menu itemsGuest3closed19.2
661TodoSkylineUpdate unimod.xml which is now about 2 years oldBrendan MacLean3open19.2
660TodoSkylinerevisit changes around ReSharper 2019.1 issues with false null check warningsBrian Pratt3open19.2
659DefectSkylineneed better handling of typing mistakes (or partially completed typing) when user is renaming a peptideBrian Pratt3open19.2
658DefectSkylinenonstandard (or at least non-intuitive) keystroke handling causes exceptionBrian Pratt3open19.2
657DefectSkylineRecord BlibBuild command-line arguments in LibInfo tablematt.chambers42@gmail.com3open19.2
656TodoSkylineadd diaPASEF supportBrian Pratt3open19.2
655DefectSkylineadjust behavior of "Explicit Retention Time" to match user expectationsBrian Pratt3open19.2
654TodoSkylineAdd support for PEFF extended FASTA format (http://www.psidev.info/peff)Brian Pratt3open19.2
653TodoSkylineImplement arbitrary peptide proportion groupingBrendan MacLean2resolved19.2
652TodoSkylineControlling the (#) suffix added to replicate filenames from a .wiff ImportBrendan MacLean3resolved4.3
651TodoSkylineDocument Settings - Reports should have buttons to manage the list or add a new reportNick Shulman3open 
650TodoSkylineAdd a menuitem to turn off MIDAS triggered spectra annotationsBrendan MacLean3open 
649TodoSkylineNeed a way for external tools to produce annotations that get imported into the current documentNick Shulman3open19.2
648DefectSkylineError when building a library from MetaMorpheus results (*.mzID)matt.chambers42@gmail.com3resolved4.3
647DefectSkylineProblems with annotations in reportsGuest2closed19.2
646DefectSkylineProblem to build library from MaxQuantmatt.chambers42@gmail.com3resolved4.3
645DefectSkylineMaxQuant mod parser will fail when first two letters are shared between 2 different modsmatt.chambers42@gmail.com3open 
644TodoSkylineAdd ability to set a minimum and maximum when generating optimization valuesBrendan MacLean3open4.3
643DefectSkylineProblem interpreting modification format found in NIST phospho librariesBrian Pratt3open19.2
642DefectSkylineBiblioSpec unicode filepath supportmatt.chambers42@gmail.com3resolved4.3
641DocumentationSkylineHow to assign report template name in Command-line argumentGuest3closed4.3
640DefectSkylineUnable to process chromatograms for the moleculematt.chambers42@gmail.com3resolved4.3
633DefectSkylineUsability idea: when we fail to open a Skyline document, check to see if it actually IS a Skyline documentGuest3closed 
632DefectSkylineFailure importing SRM runsmatt.chambers42@gmail.com3open4.3
631TodoSkylineFinding *.dat files from the spectral librarymatt.chambers42@gmail.com4resolved4.3
630DefectSkylinerdotp uses Statistics.Angle() when it should be using NormalizedContrastAngleSqrt()Brendan MacLean2open19.2
629DefectSkylineNo import due to overlapping chromatogram start times?matt.chambers42@gmail.com2open4.3
628TodoSkylineThermo RAW attribute accessmatt.chambers42@gmail.com3resolved4.3
627TodoSkylineImport results from multi-injection wiff files that have the same sample/injection namesVagisha3resolved19.2
626TodoSkylineAdd command-line arguments to select samples to import from multi-injection wiff filesVagisha3resolved19.2
625TodoSkylineLipid quant using Skyline and LipidSearchmatt.chambers42@gmail.com3open4.3